plotSpikeHI              package:CALIB              R Documentation

_p_l_o_t _h_y_b_r_i_d_i_z_e_d _t_a_r_g_e_t _v_s _i_n_t_e_n_s_i_t_y

_D_e_s_c_r_i_p_t_i_o_n:

     With final parameter setting, plot the amount of hybridized
     targets and intensities of calibration controls.

_U_s_a_g_e:

     plotSpikeHI(spike, parameter, array = 1, xlab = "log(Hybridized)",
                 ylab = "log(Intensity)", main = colnames(spike$R)[array],
                 xlim = NULL, ylim = NULL, pch = 19, cex = 0.2, 
                 cy5col = "black", cy3col = "black", noerror = TRUE,
                 noepch = 19, noecex = 0.1, noecy5col = "lightpink",
                 noecy3col = "lightblue", curve = TRUE, lwd = 1.5, 
                 curvecy5col = "red", curvecy3col = "green", ...)

_A_r_g_u_m_e_n_t_s:

   spike: a 'SpikeList' object.

parameter: a 'ParameterList' object.

   array: integer giving the array to be plotted. 

    xlab: a title for the x axis.

    ylab: a title for the y axis.

    main: an overall title for the plot.

    xlim: the x limits (min,max) of the plot.

    ylim: the y limits of the plot.

     pch: an integer code for one of plotting characters or symbols for
          the spike data set. Default is 19.

     cex: a numerical value giving the amount by which the points which
          indicate spike data set should be scaled relative to the
          default.  Default is 0.2.

  cy5col: color of points for cy5. Default is black. 

  cy3col: color of points for cy3. Default is black. 

 noerror: a logical value. If it is 'TRUE', plot the amount of
          hybridized targets assuming equal spot capacities. Default is
          'TRUE'. 

  noepch: pch for the points with equal spot capacities. Default is 19. 

  noecex: cex for the points with equal spot capacities. Default is
          0.1.

noecy5col: color for the points with equal spot capacities of cy5. 
          Default is lightpink.

noecy3col: color for the points with equal spot capacities of cy3.
          Default is lightblue.

   curve: a logical value. If it is 'TRUE', plot final parameter
          setting. Default is 'TRUE'.

     lwd: width of the parameter curves. Default is 1.5.

curvecy5col: color of the parameter curves for cy5. Default is red. 

curvecy3col: color of the parameter curves for cy3. Default is green. 

     ...: other graphical parameters can be used in function ''plot''. 

_D_e_t_a_i_l_s:

     The function plots hybridized targets vs measured intensities of
     one array. The argument  'array' gives the array index to be
     plotted. The function accepts the spike concentrations  from the
     argument 'spike' and the estimated spot error for each spot from
     the argument  'parameter'. The hyrbidized targets for each spot
     can be calculated by the following  formula: formula.

     The argument 'noerror' says whether or not the hybridized targets,
     which are calculated by the above mentioned formula assuming equal
     spot capacities, are plotted. If they are plotted, other arguments
     like 'noepch','noecex','noecy5col' and 'noecy3col' are used to 
     specify the type, the size and the color of the points.

     Estimated parameter curves can be shown on the plot. Since model
     parameters are different for two colors, two parameter curves are
     expected for one array. The funciton accepts  parameters of both
     colors from the argument 'parameter'. If the curves are plotted,
     the  arguments 'lwd', 'curvecy3col' and 'curvecy5col' are used to
     specify the width and color of the curves.

     Details for the graphical parameters can be seen in function
     'plot', 'points' and 'curve'.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     Engelen, K., Naudts, B., DeMoor, B., Marchal, K. (2006)  A
     calibration method for estimating absolute expression levels from 
     microarray data. Bioinformatics  22: 1251-1258.

_E_x_a_m_p_l_e_s:

     # load data: spike and parameter
     data(spike)
     data(parameter)

     # specify the array to be plotted.
     array <- 1

     # use the default values for other parameters
     plotSpikeHI(spike,parameter,array=array)

